changes in runner, PBS creation, makeProblemSet

* updates to PBS creations

* some changes to makeProblemSet (see diff, I don't remember what these changes
  were exactly. Were done in conjunction with Lianah, to fix some trouble we
  had with creating a problem set)

* ignoreErrors = True in runner.py (if you can't parse the stats, don't just die)
runner uses PBS_WALLTIME to quit early, other changes
fixes
added bowery-p12-runner.pbs for HPC use
Merge remote-tracking branch 'upstream/master'
Merge remote-tracking branch 'origin/master'